This invention relates to the fields of chemical design and to methods for selecting, modifying, and creating synthetic chemical structures and to their methods of use.
A critical feature of a polypeptide is its ability to fold into a three dimensional conformation or structure. Polypeptides usually have a unique conformation which, in turn, determines their function. The conformation of a polypeptide has several levels of structure. The primary structure is a linear sequence of a series of amino acids linked into a polypeptide chain. The secondary structure describes the path that the polypeptide backbone of the polypeptide follows in space, and the tertiary structure describes the three dimensional organization of all the atoms in the polypeptide chain, including the side groups as well as the polypeptide backbone.
Covalent and noncovalent interactions between amino acids determine the conformation of a polypeptide. The most common covalent bond used in establishing the secondary and tertiary structure of a polypeptide is the formation of disulfide bridges between two cysteine residues (forming cysteine). The formation of noncovalent bonds is influenced by the aqueous environment such as water. A large number of noncovalent interactions, such as van der Waals, ionic, hydrophobic and hydrogen-bonded interactions, contribute to the way in which a polypeptide folds. Hydrophobic interactions, which occur between amino acids with nonpolar side chains, are particularly important because they associate to exclude water. These side chains generally form the core of the polypeptide, where they are mostly inaccessible to water.
The secondary structure of polypeptides can be divided into two general classes: xcex1-helix and xcex2-sheet. An xcex1-helix is stabilized by hydrogen bonding and side chain interactions between amino acids three and four residues apart in the same polypeptide chain, whereas a xcex2-sheet is stabilized by hydrogen bonding and side chain interactions between amino acids more distant in a polypeptide chain and in different polypeptide chains. A complete understanding of the construction of xcex1 helices and xcex2 sheets is important for the manipulation of the structure and function of polypeptides.
A major challenge in de novo polypeptide design (more often referred to as de novo peptide design), which is the design of polypeptides (or peptides) from scratch, is the engineering of a polypeptide having the folding stability of the native structure of a natural polypeptide. Several polypeptides have been designed with the xcex1 helix as the major structural element. Few polypeptides have been designed with the xcex2 sheet as the major structural element. Unlike xcex1 helices where there is a regular succession of hydrogen bonds between amides three and four residues apart in the sequence, xcex2 sheets are formed by residues at variable and often distant positions in the sequence. In addition, they tend to form aggregates in solution and precipitate under physiological conditions. A major difficulty in designing a structurally stable xcex2 polypeptide is dealing with the interactions between xcex2 sheets.
Designing a polypeptide to form a xcex2-sheet has in the past usually been based on one of a number of structural propensity scales known in the art. These scales are derived either statistically from structural databases of known folded polypeptides or by making single or minimal site-specific changes in a fully folded polypeptide. See, for example, C. A. Kim, et al., Nature, 362, 267 (1993); D. L. Minor, et al., Nature, 371, 264 (1994); D. L. Minor, et al., Nature, 367, 660 (1994); and C. K. Smith, et al., Biochemistry, 33, 5510 (1994). However, such scales are generally less useful when designing de novo xcex2-sheet folds in short peptides where considerably more xcex2-sheet and/or side-chain surface (particularly hydrophobic surface) will be exposed to water. D. E. Otzen, et al., Biochemistry, 34, 5718 (1995).
Betabellin was one of the first de novo designed class of xcex2-sheet peptides. J. Richardson, et al., Biophys. J., 63, 1186 (1992). It was intended to fold into a sandwich of two identical four-stranded, antiparallel xcex2 sheets. A more recent version of betabellin, betabellin 14D, was designed by Yan, et al., Protein Science, 3, 1069, (1994). Quinn, et al. designed betadoublet, which is similar to betabellin but contains only naturally encoded amino acids. T. P. Quinn, et al., Proc. Natl. Acad. Sci. U.S.A., 91, 8747 (1994).
However, peptides in the betabellin and betadoublet series show limited solubility in water and minimal, highly transient xcex2-sheet structure, i.e., nonstable structures. The best betabellin made thus far, Betabellin peptide 14D, for example, becomes less soluble at pH values above 5.5 making it impractical for use at a physiological pH. Moreover the xcex2-sheet structure formed by peptide 14D relies on the presence of an intermolecular disulfide bridge to yield a dimeric species. The peptides of the present invention do not have these limitations. Betadoublet, which has the same predicted antiparallel xcex2-sheet motif as betabellin, is even less water soluble, and only at a lower pH of about 4, and fails to show any compact, stable folding, i.e., structure.
Water solubility and pH ranges are important to peptide function. A polypeptide that is not soluble under physiological conditions (i.e., in water at a pH of about 7.0-7.4 and in about 150 mM NaCl or an equivalent physiological salt) is not functional and is therefore not useful. Neither the betabellin nor the betadoublet strategies for peptide design achieved sufficient solubility, peptide compactness, or peptide self-association under physiological conditions.
Hence, there remains a need for xcex2-sheet forming peptides that are not only water soluble, but soluble at physiological conditions, and self associate.
Sepsis syndrome continues to be one of the leading causes of mortality in critically ill patients and gram-negative bacterial pathogens cause about ⅓ of these cases. Despite intensive laboratory and clinical investigation, the mortality associated with gram-negative bacterial sepsis and shock remains at about 40%, a statistic that has changed little over time. Lipopolysaccharide (LPS, or endotoxin) is an integral component of the outer membrane of gram-negative bacteria and triggers activation of macrophages that, in turn synthesize and secrete cytokines within the endogenous tissue milieu and systemic circulation. The resultant release of tumor necrosis factor-xcex1 (TNF-xcex1) and other cytokines by macrophages is causally linked to the host inflammatory response and the subsequent development of septic shock. Unfortunately, standard inflammatory response and the subsequent development of sepsis and shock, including administration of potent antibiotics, aggressive fluid resuscitation, hemodynamic monitoring, and metabolic support, has not been associated with a significant reduction in mortality.
A 27 amino acid synthetic peptide based on amino acids 82-108 of BPI significantly inhibited TNF-xcex1 secretion in vitro and administration of the peptide in animal models diminished endotoxin levels, although abrogation of TNF-xcex1 secretion was incomplete (Battafarano et al. Surgery 118:318-324, 1995 and Dahlberg, et al. J. Surg. Res. 63:44-48, 1996). The effect of anti-endotoxin monoclonal antibodies HA-1A and E5 on mortality during sepsis syndrome has been studied by phase III clinical trial. In these studies, mortality rates were not reduced as compared to placebo treatments (The CHESS trial study group, Ann. Int. Med. 121:1-5, 1994; Bone et al. Crit. Care Med. 23:994-1005, 1995). Accordingly, novel reagents are needed to treat gram-negative bacterial infections.
Tumor growth can be controlled by deprivation of vascularization (see Folkman, Natl. Cancer. Inst. 82:, 4-6, 1990 and Folkman et al. J. Biol. Chem. 267:10931-10934, 1992). A growing number of endogenous inhibitors of angiogenesis include platelet factor-4 (PF4, Gupta et al. Proc. Natl. Acad. Sci. USA 92:7799-7803, 1995), interferon-xcex3 inducible protein-10 (IP-10, Luster, et al. J. Exp. Med. 182:219-231, 1995), as well as synthetic agents including thalidomide, metalloproteinase inhibitors, and the like. There is a need for reagents to inhibit angiogenesis including agents that inhibit endothelial cell proliferation for a variety of applications, including, but not limited to tumorigenesis.
The present invention provides a method for synthesizing a water-soluble peptide having at least about 35% amino acids having hydrophobic side chains, the method comprising combining amino acids having charged side chains and amino acids having noncharged polar side chains with amino acids having hydrophobic side chains, wherein the amino acids having charged side chains are provided in a ratio of at least about 2:1 amino acids having positively charged side chains to amino acids having negatively charged side chains.
The present invention also provides a method for synthesizing a water-soluble peptide having at least about 35% amino acids having hydrophobic side chains, the method comprising combining amino acids having charged side chains and less than about 20% amino acids having noncharged polar side chains with amino acids having hydrophobic side chains, wherein: the amino acids having charged side chains are provided in a ratio of at least about 2:1 amino acids having positively charged side chains to amino acids having negatively charged side chains; the water-soluble peptide has about 35% to about 55% amino acids having hydrophobic side chains; and at least two of the amino acids having hydrophobic side chains are positioned in the peptide with an intervening turn sequence in a manner such that the two amino acids having hydrophobic side chains are capable of aligning in a pairwise fashion to form a xcex2-sheet structure; and the turn sequence is LXXGR, wherein each X is independently selected from the group consisting of K, N, S, and D. Herein, percentages are reported as the number of specified amino acids relative to the total number of amino acids in the peptide chain.
This invention also relates to a series of xcex2pep peptides prepared using the methods of this invention. These peptides are provided as xcex2pep-1 through xcex2pep-30 and correspond to SEQ ID NO:1 through SEQ ID NO:30. This invention also relates to a method for treating a bacterial infection or endotoxic shock comprising administering an amount of a pharmaceutical composition effective to inhibit the bacterial infection or neutralize endotoxin to a mammal, wherein the pharmacutical composition comprises (a) a peptide demonstrating bactericidal activity or endotoxin neutralizing activity selected from the group consisting of xcex2pep-1 through xcex2pep30 (SEQ ID NO: 1 through SEQ ID NO:30); and (b) a pharmaceutically acceptible carrier.
In one embodiment, the peptide neutralizes endotoxin, in another the peptide is bactericidal and in another the peptide is both bactericidal and neutralizes endotoxin. In a preferred embodiment, the peptide has endotoxin neutralizing acitivity and is selected from the group consisting of xcex2pep-8 and xcex2pep-23. In another preferred embodiment, the peptide has bactericidal activity and is selected from the group consisting of xcex2pep-19, xcex2pep-7, xcex2pep-4, xcex2pep-22 and xcex2pep-1.
This invention also relates to a method for inhibiting TNF-xcex1 levels in a mammal comprising the step of administering a therapeutically effective amount of a pharmaceutical composition comprising: (a) a peptide demonstrating bactericidal activity or endotoxin neutralizing activity selected from the group consisting of xcex2pep-1 through xcex2pep30 (SEQ ID NO: 1 through SEQ ID NO:30); and (b) a pharmaceutically acceptible carrier. In a preferred embodiment the peptide is xcex2pep-3.
This invention also relates to a method for inhibiting endothelial cell proliferation comprising the step of administering an effective amount of a composition comprising: a peptide demonstrating endothelial cell proliferation inhibition selected from the group consisting of xcex2pep-1 through xcex2pep-30 (SEQ ID NO: 1 through SEQ ID NO:30). In one embodiment, the composition is a therapeutically effective amount of a pharmaceutical composition comprising: a peptide selected from the group consisting of xcex2pep-14 or xcex2pep-16; and a pharmaceutically acceptible carrier.
The invention also relates to a method for promoting inter-cellular adhesion molecule (ICAM) expression comprising the step of administering an effective amount of a composition comprising: a peptide promoting inter-cellular adhesion molecule expression selected from the group consisting of xcex2pep-1 through xcex2pep-30 (SEQ ID NO:1 through SEQ ID NO:30).
xe2x80x9cAmino acidxe2x80x9d is used herein to refer to a chemical compound with the general formula: NH2xe2x80x94CRHxe2x80x94COOH, where R, the side chain, is H or an organic group. Where R is organic, R can vary and is either polar or nonpolar (i.e., hydrophobic). The amino acids of this invention can be naturally occurring or synthetic (often referred to as nonproteinogenic). As used herein, an organic group is a hydrocarbon group that is classified as an aliphatic group, a cyclic group or combination of aliphatic and cyclic groups. The term xe2x80x9caliphatic groupxe2x80x9d means a saturated or unsaturated linear or branched hydrocarbon group. This term is used to encompass alkyl, alkenyl, and alkynyl groups, for example. The term xe2x80x9ccyclic groupxe2x80x9d means a closed ring hydrocarbon group that is classified as an alicyclic group, aromatic group, or heterocyclic group. The term xe2x80x9calicyclic groupxe2x80x9d means a cyclic hydrocarbon group having properties resembling those of aliphatic groups. The term xe2x80x9caromatic groupxe2x80x9d refers to mono- or polycyclic aromatic hydrocarbon groups. As used herein, an organic group can be substituted or unsubstituted. One letter and three letter symbols are used herein to designate the naturally occurring amino acids. Such designations including R or Arg, for Arginine, K or Lys, for Lysine, G or Gly, for Glycine, and X for an undetermined amino acid, and the like, are well known to those skilled in the art.
The term xe2x80x9cpeptidexe2x80x9d or xe2x80x9cpolypeptidexe2x80x9d is used herein to refer to an amino acid polymer. A single peptide of this invention preferably has at least 20 amino acids. Preferably the peptides of this invention are no greater than 50 amino acids in length, and more preferably about 28 to about 33 amino acids in length.
The term xe2x80x9cwater-solublexe2x80x9d is used herein to refer to compounds, molecules, and the like, including the peptides of this invention, that are preferably readily dissolved in water. The compounds of this invention are readily dissolved in water if about 1 mg of the compound dissolves in 1 ml of water having a temperature of about 35-45xc2x0 C. More preferably, the peptides of this invention will have a water solubility of at least about 10 mg/ml and often of at least about 20 mg/ml. Even more preferably, the peptides are soluble at these concentrations under physiological conditions, including a pH of about 7.0-7.4 and a salt concentration of about 150 mM NaCl.
The term xe2x80x9chydrophobic amino acid side chainxe2x80x9d or xe2x80x9cnonpolar amino acid side chain,xe2x80x9d is used herein to refer to amino acid side chains having properties similar to oil or wax in that they repel water. In water, these amino acid side chains interact with one another to generate a nonaqueous environment. Examples of amino acids with hydrophobic side chains include, but are not limited to, valine, leucine, isoleucine, phenylalanine, and tyrosine.
The term xe2x80x9cpolar amino acid side chainxe2x80x9d is used herein to refer to groups that attract water or are readily soluble in water or form hydrogen bonds in water. Examples of polar amino acid side chains include hydroxyl, amine, guanidinium, amide, and carboxylate groups. Polar amino acid side chains can be charged or noncharged.
The term xe2x80x9cnoncharged polar amino acid side chainxe2x80x9d or xe2x80x9cneutral polar amino acid side chainxe2x80x9d is used herein to refer to amino acid side chains that are not ionizable or do not carry an overall positive or negative charge. Examples of amino acids with noncharged polar or neutral polar side chains includes serine, threonine, glutamine, and the like.
The term xe2x80x9cpositively charged amino acid side chainxe2x80x9d refers to amino acid side chains that are able to carry a full or positive charge and the term xe2x80x9cnegatively charged amino acid side chainxe2x80x9d refers to amino acid side chains that are able to carry a negative charge. Examples of amino acids with positively charged side chains include arginine, histadine, lysine, and the like. Examples of amino acids with negatively charged side chains include aspartic acid and glutamic acid, and the like.
The term xe2x80x9cself-associationxe2x80x9d refers to the spontaneous association of two or more individual peptide chains or molecules irrespective of whether or not the peptide chains are identical.